[ensembl-dev] JSON output missing data

[Rightmire, Michael Paul]

Hello,


I'm using the VEP command line from the Docker container with both JSON and VCF output. I've noticed that the JSON output is missing fields that are shown in the VCF file.


For example, the CSQ (from the INFO column in the VCF file) contains the gene's SYMBOL. The JSON output does not (not for any of the variants.) Both the JSON and the VCF output is from the same original VCF input file.


The sample JSON found at https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json does show a "gene_symbol" key, which is missing from my output.


The commands used to generate the two annotation outputs were...?

vep  --cache  --dir_cache=/opt/vep/.vep  -i  "/path/$filename"  -o  "/path/${filename}.annotated.vcf"  --offline  --vcf  --force_overwrite

vep  --cache  --dir_cache=/opt/vep/.vep  -i  "/path/$filename"  -o  "/path/${filename}.annotated.json"  --offline  --json  --force_overwrite


Should I be using additional switches to get the comparable output?


Thanks!

Mike


Michael Rightmire

Bioinformatics and Omics Data Analytics (B240)

Omics Software Architect


German Cancer Research Center (DKFZ)

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 176 7131 8758

fax: +49 6221 42-3563


M.Rightmire at dkfz-heidelberg.de<mailto:m.mustermann at dkfz.de>

www.dkfz.de<http://www.dkfz.de/>
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